AMBER Archive (2008)

Subject: AMBER: questions about previous posts

From: Naser Alijabbari (
Date: Mon Aug 11 2008 - 23:17:40 CDT


Someone else in my group has written the code to take the output of ptraj
eigen frequencies and calculate absorption coefficients. Feel free to answer
what you have time for and thanks before hand.

My questions:

1) is a discussion about
the difference btw Langevin vs Berendsen temperature control. The end
conclusion is that Langevin corrupts the fast dynamics of the system so it
shouldn't be used during production run, and if one wants to compute time
correlation function then they need to avoid ntt=3. Can anyone elaborate on
this? From the tutorial I was under the impression that Berendsen algorithm
had to be much more elaborate, so is my last step correct? My main focus is
picking up vibrations occurring in a time frame of ~6ps, is it a good idea
to use ntt=3 at all for this type simulation?

100ps simulation of the protein 2TRX w/ 108 residues, AMBER 8


set default Dielectric constant

TIP3PBOX w/ 8 angstrom water

I get the following warning because I don't add Na+ ion "WARNING: The
unperturbed charge of the unit: -4.000000 is not zero". I neutralize DNA but
I am not sure if the guideline applied to everything (does it cause problems
with periodic boundary condition?)



maxcycle=1000, ncyc = 500,

ntx=1, (default)

ntpr=100 (default is 50 for writing to mdinfo)

ntr= 1,


cut =10.0,


imin = 1,
maxcyc = 2500, ncyc = 1000,
ntb = 1,
ntr = 0,
cut = 10

Step 3:


irest=0, ntx=1,

ntwr=1000, ntwx=100, ntpr=100,

ntr= 1,

ntslim=8000, dt=.002,

ntt=3, gamma_ln = 1.0, temp0=300, tempi=0,


ntc=2, ntf=2, cut =10.0,

Step 4:


irest=1, ntx=5

ntwr=1000, ntwx=1000, ntpr=100,


ntslim=20000, dt=.002,

ntt=3, gamma_ln=1, temp0=300, tempi=300,

ntb=2, pres0=1, ntp=1, taup=2

ntc=2, ntf=2, cut=10

Step 5:


irest=1, ntx=5,

ntwr=1000, ntwx=1000, ntpr=100,


ntslim=30000, dt=.002,

ntt=3, gamma_ln=1, temp0=300, tempi=300,

ntb=2, pres0=1, ntp=1, taup=2,

ntc=2, ntf=2, cut=10,

Production run:


irest=1, ntx=5,

ntwr=1000, ntwx=25, ntpr=100,


ntslim=50000, dt=.002, ncsm=1

ntt=1, temp0=300, tempi=300,

ntb=2, pres0=1, ntp=1, taup=2,

ntc=2, ntf=2, cut=10


trajin bbprotein.mdcrd.gz

strip :WAT

trajout bbproteinNOwat.mdcrd

rms first out bbprotein.rms @C,CA,N time .05

matrix mwcovar name bbprotein.matrix out bbprotein.matrix

analyze matrix bbprotein.matrix out bbprotein.mode vecs 400

I am moving the center of mass at every step based on someone else's
example, and I am not sure if it makes a difference to do this during
simulation or in my ptraj. There is a discussion wrt to "pca analysis" and I am not sure if it
applies. Center of mass was also discussed here and it suggests that it is
not necessary to do this if one is using ntt=1. Any hints?

2) and says
that if one averages the results and the simulation is long enough two
machines or different number of processors will give the same result. What
is averaged? And what is long enough? Is there a rule of thumb?

3) is a discussion about
doing multistep production runs (i.e. doing a simulation from 0 to 100ps and
feeding the .rst file to the input of another simulation from 100 to 200ps
or a 200ps in two 100ps steps). Discussion points out that during
calculation higher precision is used than what is written to the .rst file.
This truncation doesn't seem to shift the position of the absorption peaks
for me. However, there is a significant difference between doing a 0 to
200ps run vs 0 to 100ps fed to 100 to 200ps. So a multi step simulation is
less accurate?

4) is a
discussion about regularity of writing to mdcrd during production run. As I
mentioned before I am interested in the molecular vibrations within ~6ps
time frame. Does this mean that at max. I can get away w/ writing to mdcrd
every 3000 step (ntwx=3000, dt=.002)? Also does it make a different what
value one uses for vecs? I picked a value from an example but I am not sure
what the preference is.

I can't seem to make the absorption coefficients vs cm^-1 plot to settle on
any value since position of absorption peaks change w/ number of processors,
time duration, steps in simulation.



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